


Unseen Complications

by Ironlad2045



Category: Brooklyn Nine-Nine (TV)
Genre: Alternate Universe - Canon Divergence, F/M, Gen
Language: English
Status: In-Progress
Published: 2019-07-02
Updated: 2019-10-09
Packaged: 2020-06-02 23:43:12
Rating: Mature
Warnings: Graphic Depictions Of Violence
Chapters: 2
Words: 4,948
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/19451929
Author URL: https://archiveofourown.org/users/Ironlad2045/pseuds/Ironlad2045
Summary: -Shit!-.He yelled, hitting the table in the interrogation room. He was in the opposite side of the table he was used to, cuffed, looking his reflection in the fake mirror, just as all the perps he arrested across the years. How did I get in this situation he asked himself. He knew the exact answer.AU where Jake's undercover operation lasts a lot more than expected and he finds different complications he did not expected when he took the assigment.





	1. Between a Rock and a Hard Place

**Author's Note:**

> This is my first work ever, so take that in mind. The story is more or less set in season 3, at least for the first few chapters there are going to be some flashbacks centered around Jake. There are many differences with canon because Jake wasn't in the precinct for the last years. Hope you enjoy It.

"Shit!". He yelled, hitting the table in the interrogation room.

He was in the opposite side of the table he was used to, cuffed, looking at his reflection in the fake mirror, just as all the perps he arrested across the years. How did I get in this situation he asked himself. He knew the exact answer. 

* * *

_2 years and 5 months and 20 days earlier_

Jake Peralta’s life have not been easy his father left him and his mother at a young age. In school he was never part of the popular kids, he was not really part of any group at all. However, when he became a cop his life completely changed for the better, he found purpose and appreciation in his job. He made good friends, including someone he could see as a real father whose advise he trusted more than anything (well almost), that was the main reason he got himself in this situation. But most importantly he met her, Amy Santiago. A beautiful and intelligent woman, cute in all possible ways, someone whose opinion he valued more than anything. However, by the time he realized how he felt she was with Teddy. Oh, how he hated Teddy, you could add him to the list of reasons he took this assignment, which made him leave his dream job.

Long story short Jake Peralta got himself fired of the NYPD in order to work with the FBI in an undercover operation that could do a lot of good for the city. Because the nature of this op none of his friends in the 99 could know the real reason from him leaving, the only one who did know about the operation was Captain Holt, but he would not have any form of contact with Peralta while he was undercover. In other words, Jake was completely alone, and he felt like it. Knowing he was not going to come back in a long time, maybe ever, he decided to say goodbye to Amy, which was going to be even more difficult after all the insults directed to cops he yelled while leaving the precinct in order to set up his cover as a mad fired detective.

"Hey". He said, when he finally found her in the parking lot minutes before going home.

"If it isn’t mister, I hate cops now". She responded, looking at him with annoyance in her face but he could also see sadness and betray in her eyes, very similar to the way he looked when his father left. "What do you want Peralta? ". But even like that she looked more beautiful than any woman he had ever seen.

"Amy, I…". He stopped, if he chose the wrong words, he could blow his cover jeopardizing the operation. "I just wanted to say that I wished that something happened between us, romantic styles". Her annoyance changed to surprise. "But I understand that you are with Teddy now and with me being fired and all I don’t.......think that we are going to talk for a long while……so this is goodbye, I guess.". Rejection would be too painful right now and he didn’t want her to feel obligated to say anything. So after that he just kept walking leaving her without the chance to answer.

His next stop was going to a bar where he would meet some members of the mafia and with some luck become one of them. As it turned out, luck was on his side, by acting extremely drunk (he was only a little drunk) and telling them his story he got in. His job was simple, drive around a minor guy in the mob. Because his knowledge of the neighborhood and his past as a detective in the 99 his bosses kept him in Brooklyn.

Every day since his last “conversation” with Amy flew for Jake, by the time the 6 months the op was supposed to last were over he had barely got any information with little to no evidence on some minor members of the mafia. The assignment was going to take more time.

  
If he wanted to go back to his life, he needed to make more progress fast. And one day he got his chance.

* * *

_Present_

The sound of the door crashing brought him back to the present. He knew the procedure in cases like this, sooner or later a detective would come to question him, he only hoped it wasn’t her, he didn’t feel ready to see her again just yet.

  
The detective who just entered the interrogation room and smashed the door was Rosa Diaz, it made sense. She met Jake in the academy making them good friends which meant she knew a lot of things about him but could also be objective while interrogating him, she wouldn’t put their friendship first unlike Charles or Terry.

**"** So **"**. She looked at him the way she would look any other perp she caught. "The mob now hires failed cops?" . She dropped the file she held in her hand in the table and seated on the chair in front of him,

Diaz was a good detective and she knew how to press his buttons, if his cover was real the mention of him as a failed cop would probably work. Lucky for Jake it wasn’t, but Rosa didn’t know he was “fired” to work with the FBI. How could he get out of this situation?, the easy way out would be telling her about his real mission, if she didn’t believe him she could just go and ask Captain Holt.

Then he realized, where the hell was Captain Holt?. Surely, he would be the one to interrogate him in order to help him get out or something like that. He didn’t know what had happened in the precinct in the last years, maybe Holt wasn’t appointed to the 99 anymore.

"I asked you a question! ". She yelled hitting the table with her left hand. Rosa may have always been good hiding her emotions, but not this time. She was furious and he could tell. She obviously expected him to jump or show a reaction to the hit, but he stood there motionless looking at her right in the eyes. His time in the mafia had changed him.

Okay so logic said Holt wasn’t at the precinct, the best shot he had was waiting for him to come to aid him. So, he needed to buy time.

**"** Well Flowers, I am just a normal, innocent civilian. I have no idea what you are talking about." . He responded with a smirk in his face. He wanted to maintain his cover as an asshole detective that was fired from the force. And if he confessed he worked for the mafia he would go to prison.

  
"My name is Detective Diaz, you call me Flowers again and I will hit that smirk off your face-. He knew she hated being called Flowers, because in the academy one of their instructors came up with that nickname after hearing her name. 

  
In response to her threat he only laughed. If she told him that 2 years ago, he would certainly back off, but now it barely had any impact on him. He knew laughing would make her angrier.

"Cut the shit Jake, you know we got you. We have evidence you have been working for the Ianuccis for the last two years, and we know you have ties to some of the big guys"

  
"I have no idea what you are talking about _detective"_. He said detective with a stupid silly voice that he knew she wouldn’t like at all.

  
As he expected she saw him with fury.

"You were caught in a building full of crates with guns and heroin, we have been scouting the place for months". She showed him some pictures from the file of the building and the crates. "We caught 13 other guys with previous felonies, some have served time for murder. Now look at this". She took other pictures from the file. "This is the gun we found you with, it has your prints all over and it was missing 5 bullets, the exact number of gunshots that prevented our strike team from rushing the position they found you in. Which translates to you shooting police officers". She made a pause, the hate in her look changed to concern.

"You know what that means Jake, you could go to jail for 25 years or more. You have two choices you can either play ball with us by helping us take down your mafia or you can keep being an asshole and rot in jail. Your choice". Her voice broke a little bit with the last words. He could swear her eyes were a little red, she stood up and left. Smashing the door again in her way out. He felt bad about hurting his friends, but everything would be cleared soon enough.

Still, Jake Peralta was screwed. The evidence was there, he could get charged and put on trial. The FBI would help him, so there was no way he was going to jail. But that meant the nature of his mission would be revealed and all his work would be for nothing, not everyone would go down with the ship. And he was so close.

"Jake Peralta you have 2 choices, you can either talk to Rosa about your assignment which would get you out of trouble but it would make all your work for the past 2 years worthless or you can wait for Holt to show up and get you out of here so you can get back to work, but if he doesn’t come soon you will probably end up getting charged and by the time everything is cleared your work for the last 2 years will be worthless. Dammit Holt! You better come back soon". He said to himself.

At least the worst part was over. The interrogation was over for now, his situation could only get better from here on now. He just had to seat there and wait for Holt to come, worst case scenario Rosa would come back to see if he had made up his mind.

That is what he truly thought until half an hour after Rosa left, she came in. Amy Santiago, the only person he thought about every day for the last 2 years and 5 months, the one who he missed the most. If he could only tell her the true about the last 2 years.


	2. Chapter 2

**Notes for the Chapter:**

> Thanks for the support in the first chapter. 
> 
> October 9 update.  
> So I haven't updated this work for months. Mostly because writers block. And because I rushed this second chapter initially I wasn't happy with the results so I decided to edit it, I added a lot so it is completely different. After some suggestions I also edited a few thing in the first chapter too. I can't promise I will update this work every few weeks but I'll try my best.

Jake Peralta believed that everything was going to be alright, Captain Holt would eventually come and get him out somehow. He would go back with his cover intact and get the little evidence he needed to tear down the whole mafia. Then he would come back to his normal life, everything would go back to normal with his friends after some apologies of course.

And with some luck, just a little bit of luck, by the time all that happened Amy was going to be single again and maybe he would get a chance with her. One chance is all he needed. But Jake Peralta was wrong, everything was not going to be alright.

When Amy Santiago entered the interrogation room the way he pictured his life in a few weeks was completely shattered. She looked exactly like she did 2 years ago (pantsuit, ponytail) at least as beautiful as he remembered. The difference was now she hated his guts, the look she had was a mix of sadness, betrayal and anger. Of course she felt betrayed, her partner and one of her best friends became the very same thing they were trained to put in jail. If he didn’t manage to be an asshole to her in order to prevent her from asking too many questions his cover would be blown.

But then he entered the room holding two coffees. Teddy Wells, fucking Teddy was here in the 99. He was probably transferred sometime after Jake got fired. The 99 needed a detective, Teddy was a pretty good one and he had reasons to transfer. It seemed they were still together. Their relationship lasted a lot more than Jake would have hoped. Then it hit him, what if they were married, his heart felt like it was being thorn open.

“Well, if it isn’t Detective Santiago and Detective Goods. How it feels to be the replacement for the great detective Peralta, Teddy? Are you sure you are not overextending yourself?” said Jake with a grin in his face. 

Teddy was about to make a response to his comment when his phone rang, he quickly put the coffees on the table took his phone out of his pocket and answered.

“Captain, give me a second”. He gave a gesture to Amy and left the room. With the only person he wanted to be an asshole in the room gone he was back to freaking out about the thought he had earlier.

“Come on Peralta you are a detective look at the clues”. He started having a conversation with himself in his mind. “Let’s see, he came in with two coffees which doesn’t mean anything, he could do that as her colleague. Mmm she has her hands crossed behind her so I can’t see if she has a ring. By the time I left they were probably together for about 3 months if I remember correctly, if you add that to the 2 years and 5 months since then, they have been together for almost 3 years, too short for Santiago to agree to marry him. Just planning for the wedding would probably take 1 year, but wait, she is Amy Santiago, she could organize a huge wedding in 24 hours with time to spare. Still, the Santiago I know would probably be with a guy for 3 years or more before she even considered getting married. It would mess up her life calendar. As usual she would overthink the hell out of it. I know they are still together, if they broke up, they couldn’t work together, at least not like direct partners. I don’t know about Teddy but Amy sucks at handling awkward situations, situations just like the one her and I are in right now, that explains why she is avoiding eye contact and is standing so far from me.

Amy was “checking” something in her phone. The silence between the two became even more awkward, she should be interrogating him, trying to get him to cooperate with the police, instead she stood far from the table looking at everything in the room but him. Amy couldn’t bring herself to do it, at least not yet.

Teddy came back about 2 minutes later. He took one of the coffees he previously left on the table and gave it to Amy, then he seated in front of Jake.

“Let’s begin. Jake Peralta. I am Detective Wells and this is Detective Santiago. As Detective Diaz already told you with the evidence we have you are looking at 25 years in jail.”

“At minimum”. Amy murmured in a low voice.

“If you want to leave this room without handcuffs cooperating with the police is your only choice. Because of this Detective Santiago and I came to offer you…- He was interrupted by Jake’s loud laugh. “What is so funny? “ he asked him with a serious look on his face.

“Well _Detective Wells_ ” He said it in a very fake loud voice, very similar to the voice of narrators in old movie trailers. “I just think that’s funny how fast you want to cut a deal with me, I haven’t been arrested for even one day. It’s so clear you don’t have shit on this mafia you say I work for. You are very desperate.”

Just before Teddy replied Jake interrupted again.

“Before they fired me, they should have at least found a decent replacement. I don’t think even Santiago can carry the weight of a useless detective like yourself. She needs a dect partner.”

Just like that Jake got under Teddy’s skin. He could see the anger in his eyes, one of his hands closed into a fist. Teddy went from a smart and controlled detective to a ticking bomb. It was easier than he thought it would be.

“Stop with the bullshit!". She hit the table. “You are just wasting time. You are smart enough to know we are your last chance to not live in prison for the rest of your live with all the criminals you put there”. No longer was she avoiding any way of contact with him, she was now talking to him with her usual interrogation voice, leaning with both hands on the table and looking at him directly in the eyes with nothing but hate.

Jake laughed.

“I always knew that Santiago was the one who wears the pants in your relationship." Jake responded with a grin. Just in the moment Teddy was about to say something Jake interrupted again. “Also, If I’m wasting anyone’s time is yours, because I have time to spare”. That wasn’t true.

“From the moment you were arrested you exactly had 24 hours before you were prosecuted, trialed and sent to prison, normally you would have 48 hours, but your case is special because you were a detective.” He pulled his left sleeve up revealing a steel watch” According to my watch here, you have been in this interrogation room for about 4 hours. The next thing is very important so I’m going to tell you in words you can understand: your time is running out”. Jake really hated this guy.

He knew Teddy wasn’t that bad. But Jake really hated seeing Amy with Teddy, not because he just wanted her to be with him and with nobody else or some possessive crap like that. Seeing him with her just reminded him of many insecurities and faults he saw in himself, the things that would prevent him from being with Amy.

While Teddy was organized, Jake wasn’t. While Teddy was responsible, Jake wasn’t. While Teddy was the perfect man for Amy in every aspect. Jake wasn’t. So, if he was being an asshole with Teddy it was in order to maintain his cover.

It wouldn’t look good for the NYPD if one of their own turned after being fired by working for one of the biggest crime families in the city. By reducing the time before prosecution, they reduced the possibility of the case getting a lot of attention from the press. The faster he got in jail, the faster could they get the entire thing behind.

Being realistic the only way he was going to escape a police station was during the night, officers were tired and less alert, and he could just dive into the shadows of the city. He had to escape before morning came, that was about 6 hours from now.

“Peralta” he focused all his attention when she said his name. “You know you are guilty and there is no way you go out as a free man without our help. You can either cooperate with us by giving out information of your bosses or have a horrible life in prison. Which is it going to be?”. She looked him right in the eyes, he felt lost. But he needed managed to focus again.

Jake already thought about all that would happen to him if he really worked for the mafia, got arrested and didn’t speak, prison that’s what would happen to him most likely. But he was in an undercover operation, when the news reached agent Clarke, he would explain the situation. He wasn’t scared of jail; he feared what would happen to the operation if he didn’t get out on time.

Which is it going to be?, the question kept repeating on his mind. While the threats didn’t have any effect on him something did. Teddy’s watch, it brought some memories back. Memories he pushed back for more than a year.

Different images came directly into his mind, a brown car, a revolver, a piece of lasagna, a broken window, a bloody steel watch and a bell.

It became hard to breath, a deep pain invaded his right shoulder. As he drifted off he could hear Teddy speaking, probably asking him questions.

“Hey!”. Car. “HEY!”. Revolver. “Peralta!”. Broken Window. Bell.

“Jake!” her voice brought him back to reality.

“Huh?” he managed to mumble.

“What the hell is wrong with you?” he asked.

“Oh nothing, is just that Teddy you are sooooo boring I almost fell sleep. You seriously don’t get tired of this guy Santiago?”

The bomb exploded, Teddy quickly got up and pulled Jake from his t shirt. His right fist was 2 seconds away from Jake’s face when Amy pulled him back from the table. Yeah maybe he pushed too far.

Amy saw Teddy with confusion and anger, she quickly took him by his arm and left the interrogation room.

Jake with nothing else to do continued with his asshole persona.

“I’M SO GOING TO SUE YOU!”

* * *

As they left the interrogation room, Rosa came out from the adjacent room. She saw what happened through the fake mirror.

“What the fuck Teddy?”. Rosa yelled; she was clearly angry. If she was angry because what Teddy almost did could cause the precinct a lot of problems or because he almost hit one of her best friends wasn’t clear.

“Rosa I’ll take care of this.” Amy said with confidence.

Rosa clearly wasn’t done with her screaming, but she trusted Amy.

“I’ll see if I can prevent a sue on your stupid ass”

The female detective walked away.

“What the hell happened in there?” She practically yelled. “You almost assaulted a suspect”.

“Come on Amy there is no chance that guy is innocent.”

“Still, that’s police brutality. If you laid one finger on him even if we proved he was guilty the precinct would be in serious trouble.” She showed the frustration in her voice. “You are never like these, did those things he said about you really affected you?”

“Of course, they did, and you know why”. He looked directly into her eyes.

“I thought we got over that”. She said in frustration.

* * *

**_2 years and 4 months earlier._ **

“So this guy I met in the conference told me about this new method to brew…………..”

Amy stopped paying attention, after all it was just going to be another stupid story about pilsners. And her thoughts were driving her to that night again. The night she last saw Jake Peralta.

It had been a month since he got fired and vanished from the face of the Earth. Him missing form the precinct was very noted. His laugh, pranks and absurd comments were missed by everyone.

If she wasn’t confused enough with all the events in that day at the end of it her partner said she liked her, romantic styles. Now every once in a while, her mind would take her to Jake, the way he looked when he was cracking a case, his laugh, his smile. She didn’t understand why she was having these thoughts, but she was having them. And they were affecting her current relationship.

Teddy was a great guy, they had so much in common. At the beginning it was great, but lately she felt confused about her feelings towards him too. His stories stopped being interesting, their date routine became well a routine. Movies at Tuesdays and Thursdays and dinner at Friday or Saturday.

Amy Santiago, a woman who usually had every tiny aspect of her life planned, didn’t know what to do. She couldn’t breakup with Teddy because she didn’t know why she wanted to do it or even if she wanted to do it at all. She couldn’t talk with Jake about everything because she couldn’t find him.

Her days were reduced to a somber precinct with a huge hole at day and a somber apartment with boring stories at night.

“Hey! Amy?”. He put his hand in her shoulder.

“Huh?”

“Are you even listening to me?”. He said with annoyance in his voice.

“Of course….mmmm you were talking about pilsners?.” She tried her best to not roll her eyes because of the mention of pilsners.

“Good guess but that is no longer the point. You have been acting weird for the last few weeks. Is everything okay?” 

He was a detective which meant he could read her without much trouble. If she lied, he was going to see right through her.

So, she just confessed what happened between her and Jake the night he was fired.

“Why the hell you didn’t tell me before?”. His voice was full of anger and jealousy.

“I didn’t know how you would take it.” He was pacing throughout the room.

“So, what does his “confession” has to do with us?”

“I don’t know, I just feel confused.”

“What!, so you do like him?.” His voice got more tense.

“No is not like that. I’m confused by everything that happened that day.”

“Is not that confusing Amy, Peralta screwed up and got himself fired, end of the story.” He practically yelled.

“I just feel like our relationship is out of sync. I need some time to think things through.”

He looked directly into her eyes for a second before yelling “Fine” and leaving her apartment smashing the door in his way out.

Amy felt overwhelmed, Teddy reacted worse than she thought he would. He was a good guy he didn’t deserve this. At least now that she was alone with her thoughts, she may be able to figure everything out.

* * *

**_Present_ **

She hadn’t seen Jake in more than 2 years. Now she is doing it from the other side of the fake mirror. She thought that maybe he moved out of the city, as far from the 99 as possible. She didn’t think that he joined the Ianucci crime family. She didn’t think he could become a criminal. How did it happen?

His hair was very short, preventing it from curling, his body looked stronger, his clothes were practically the same, a blue plaid shirt and dark jeans. She could see he had some small scars in his face. The same went for his hands, specially the knuckles. But the biggest change she perceived was in his attitude, his face most of the time was serious and inexpressive. He wasn’t nervous or scared.

Amy knew that look; she could see the gears turning in his head. He was cracking a case, but she didn’t have any idea which case could it be.

“Are you sure you are okay with doing the interrogation alone?” Rosa asked from her right.

She wasn’t, she wasn’t even sure of doing the interrogation with Teddy, but that was the only way to get the answers she wanted.

“Yeah, I kno…knew him. I think I can make him cooperate. At least I have a bigger chance than Terry or Charles.”

“Fair enough. I have to go back to the docks to check the crime scene again.” Rosa got closer and murmured. “Don’t let anyone but you enter the room. That includes Wells.”

“Don’t worry. Text me if you find anything.”

Rosa gave her a nod and left. She put her eyes back on him.

_"Man I dont' know how Batman does it is super scary up here" he said as he stood in the highest point of the rooftop. Amy laughed_

_"Hey would you grab my binoculars they are in my stake out bag"_

_"Your stake out bag is 98% nuts"_

_"I get snaky, besides nuts are super healthy they are like 0% fat"._

_"Jake thats not true at all is actually the opposite"._

_"What? that nut vendor lied to me!". She laughed again._

_An entire night at the dispose of Jake Peralta because she lost an stupid bet, and it was turning out to not be as bad as she imagined._

_"The car is a piece of crap, why do you love it so much?"_

_"I was 2 days out of the academy, super nervous. Saw this guy run out of a bodega clutching a bunch of cash, so i pursue him on foot, 11 blocks!. I finally catch him, cuff him and throw him up against that car. Turned out there was for sale sign in the window and it being the best day in my life I bought it."_

_That night for the first time Amy saw her partner in a different way. Before she saw him as a goofy, child-like colleague. Now as he told that personal story she saw through him. Sure, he was goofy but he was so much more under that mask he built for himself. He was passionate about his job. He was passionate about his friends. He was passionate about this little stupid date that was supposed to be terrible._

_"Thus began the debt"_

_"Crushing debt". She corrected._

_He looked at her and smiled._

_"You do know me"_

That wasn't true anymore, so much had changed since that cold night. 

Amy needed to undertand how did everyhitng changed. That was the important question. How did Jake Peralta got himself fired from the NYPD, how her goofy partner became a top member of one of the biggest crime families in the city. How did he stay hidden for 2 years. How could she get him to cooperate with the police so he wouldn’t go to prison.

How was she going to be able to treat one of her best friends as a criminal.

**Notes for the Chapter:**

> Hope you liked it. Leave your thoughts in the comments. Kudos are very appreciated.

**Author's Note:**

> Thank you for reading, leave your thoughts in the comments.


End file.
